Current opinion in structural biology最新文献_第7页

Chemical cross-linking and mass spectrometry enabled systems-level structural biology 化学交联和质谱技术实现了系统级结构生物学。

IF 6.1 2区生物学

Current opinion in structural biology Pub Date : 2024-06-26 DOI: 10.1016/j.sbi.2024.102872

Luke Botticelli , Anna A. Bakhtina , Nathan K. Kaiser , Andrew Keller , Seth McNutt , James E. Bruce , Feixia Chu

{"title":"Chemical cross-linking and mass spectrometry enabled systems-level structural biology","authors":"Luke Botticelli , Anna A. Bakhtina , Nathan K. Kaiser , Andrew Keller , Seth McNutt , James E. Bruce , Feixia Chu","doi":"10.1016/j.sbi.2024.102872","DOIUrl":"10.1016/j.sbi.2024.102872","url":null,"abstract":"<div><p>Structural information on protein–protein interactions (PPIs) is essential for improved understanding of regulatory interactome networks that confer various physiological and pathological responses. Additionally, maladaptive PPIs constitute desirable therapeutic targets due to inherently high disease state specificity. Recent advances in chemical cross-linking strategies coupled with mass spectrometry (XL-MS) have positioned XL-MS as a promising technology to not only elucidate the molecular architecture of individual protein assemblies, but also to characterize proteome-wide PPI networks. Moreover, quantitative <em>in vivo</em> XL-MS provides a new capability for the visualization of cellular interactome dynamics elicited by drug treatments, disease states, or aging effects. The emerging field of XL-MS based complexomics enables unique insights on protein moonlighting and protein complex remodeling. These techniques provide complimentary information necessary for in-depth structural interactome studies to better comprehend how PPIs mediate function in living systems.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102872"},"PeriodicalIF":6.1,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141466793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Increased throughput in methods for simulating protein ligand binding and unbinding 提高模拟蛋白质配体结合和解除结合方法的处理量。

IF 6.1 2区生物学

Current opinion in structural biology Pub Date : 2024-06-25 DOI: 10.1016/j.sbi.2024.102871

Syeda Rehana Zia , Adriana Coricello , Giovanni Bottegoni

引用次数: 0

Quantum mechanical-based strategies in drug discovery: Finding the pace to new challenges in drug design 基于量子力学的药物发现策略：找到应对药物设计新挑战的步伐

IF 6.1 2区生物学

Current opinion in structural biology Pub Date : 2024-06-23 DOI: 10.1016/j.sbi.2024.102870

Tiziana Ginex , Javier Vázquez , Carolina Estarellas , F.Javier Luque

{"title":"Quantum mechanical-based strategies in drug discovery: Finding the pace to new challenges in drug design","authors":"Tiziana Ginex , Javier Vázquez , Carolina Estarellas , F.Javier Luque","doi":"10.1016/j.sbi.2024.102870","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102870","url":null,"abstract":"<div><p>The expansion of the chemical space to tangible libraries containing billions of synthesizable molecules opens exciting opportunities for drug discovery, but also challenges the power of computer-aided drug design to prioritize the best candidates. This directly hits quantum mechanics (QM) methods, which provide chemically accurate properties, but subject to small-sized systems. Preserving accuracy while optimizing the computational cost is at the heart of many efforts to develop high-quality, efficient QM-based strategies, reflected in refined algorithms and computational approaches. The design of QM-tailored physics-based force fields and the coupling of QM with machine learning, in conjunction with the computing performance of supercomputing resources, will enhance the ability to use these methods in drug discovery. The challenge is formidable, but we will undoubtedly see impressive advances that will define a new era.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102870"},"PeriodicalIF":6.1,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24000976/pdfft?md5=f828d7ecdbd34fd28c30ce96229060ef&pid=1-s2.0-S0959440X24000976-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141444643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Long non-coding RNAs in the nucleolus: Biogenesis, regulation, and function 核仁中的长非编码 RNA：生物发生、调控和功能

IF 6.1 2区生物学

Current opinion in structural biology Pub Date : 2024-06-22 DOI: 10.1016/j.sbi.2024.102866

Shuo Han , Ling-Ling Chen

引用次数: 0

Molecular models of bidirectional promoter regulation 双向启动子调控的分子模型

IF 6.1 2区生物学

Current opinion in structural biology Pub Date : 2024-06-20 DOI: 10.1016/j.sbi.2024.102865

Sarah Nemsick , Anders S. Hansen

引用次数: 0

Cryo-focused ion beam for in situ structural biology: State of the art, challenges, and perspectives 用于原位结构生物学的低温聚焦离子束：技术现状、挑战和前景

IF 6.8 2区生物学

Current opinion in structural biology Pub Date : 2024-06-19 DOI: 10.1016/j.sbi.2024.102864

Alex J. Noble, Alex de Marco

{"title":"Cryo-focused ion beam for in situ structural biology: State of the art, challenges, and perspectives","authors":"Alex J. Noble, Alex de Marco","doi":"10.1016/j.sbi.2024.102864","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102864","url":null,"abstract":"<div><p>Cryogenic-focused ion beam (cryo-FIB) instruments became essential for high-resolution imaging in cryo-preserved cells and tissues. Cryo-FIBs use accelerated ions to thin samples that would otherwise be too thick for cryo-electron microscopy (cryo-EM). This allows visualizing cellular ultrastructures in near-native frozen hydrated states. This review describes the current state-of-the-art capabilities of cryo-FIB technology and its applications in structural cell and tissue biology. We discuss recent advances in instrumentation, imaging modalities, automation, sample preparation protocols, and targeting techniques. We outline remaining challenges and future directions to make cryo-FIB more precise, enable higher throughput, and be widely accessible. Further improvements in targeting, efficiency, robust sample preparation, emerging ion sources, automation, and downstream electron tomography have the potential to reveal intricate molecular architectures across length scales inside cells and tissues. Cryo-FIB is poised to become an indispensable tool for preparing native biological systems in situ for high-resolution 3D structural analysis.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102864"},"PeriodicalIF":6.8,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959440X24000915/pdfft?md5=facf3fbca25e633e212221fe7b841068&pid=1-s2.0-S0959440X24000915-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141429118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advances in cryo-ET data processing: meeting the demands of visual proteomics 低温电子显微镜数据处理的进展：满足视觉蛋白质组学的需求。

IF 6.8 2区生物学

Current opinion in structural biology Pub Date : 2024-06-17 DOI: 10.1016/j.sbi.2024.102861

Abigail J.I. Watson , Alberto Bartesaghi

引用次数: 0

Nuclear periphery and its mechanical regulation in cell fate transitions 细胞命运转换中的核外围及其机械调控

IF 6.8 2区生物学

Current opinion in structural biology Pub Date : 2024-06-17 DOI: 10.1016/j.sbi.2024.102867

Rebecca K. Stephens, Yekaterina A. Miroshnikova

{"title":"Nuclear periphery and its mechanical regulation in cell fate transitions","authors":"Rebecca K. Stephens, Yekaterina A. Miroshnikova","doi":"10.1016/j.sbi.2024.102867","DOIUrl":"10.1016/j.sbi.2024.102867","url":null,"abstract":"<div><p>Cell fate changes require rewiring of transcriptional programs to generate functionally specialized cell states. Reconfiguration of transcriptional networks requires overcoming epigenetic barriers imposed by silenced heterochromatin in order to activate lineage-specific genes. Further, cell fate decisions are made in a tissue-specific context, where cells are physically linked to each other as well as to the connective tissue environment. Here, cells are continuously exposed to a multitude of mechanical forces emanating from cellular dynamics in their local microenvironments, for example through cell movements, cell divisions, tissue contractions, or fluid flow. Through their ability to deform cellular structures and activate receptors, mechanical forces can be sensed at the plasma membrane, but also at the nuclear periphery through direct or cytoskeleton-mediated deformation of the nuclear envelope. This deformation and the associated signaling is capable of triggering changes in the mechanical state of the nuclear membranes, the organization and rigidity of the underlying nuclear lamina, compaction state of chromatin, and ultimately transcription. This review focuses on the role of nuclear architecture, particularly the nuclear lamina-chromatin interface, and its mechanical regulation in cell fate decisions as well as its physiological role in development and cellular reprogramming.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102867"},"PeriodicalIF":6.8,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141418295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-molecule fluorescence imaging of DNA maintenance protein binding dynamics and activities on extended DNA 扩展 DNA 上 DNA 维护蛋白结合动态和活动的单分子荧光成像

IF 6.8 2区生物学

Current opinion in structural biology Pub Date : 2024-06-15 DOI: 10.1016/j.sbi.2024.102863

Elizabeth Marie Irvin , Hong Wang

引用次数: 0

DNA topology: A central dynamic coordinator in chromatin regulation DNA 拓扑学：染色质调控的核心动态协调器

IF 6.8 2区生物学

Current opinion in structural biology Pub Date : 2024-06-14 DOI: 10.1016/j.sbi.2024.102868

Shuai Li, Charan Vemuri, Chongyi Chen

{"title":"DNA topology: A central dynamic coordinator in chromatin regulation","authors":"Shuai Li, Charan Vemuri, Chongyi Chen","doi":"10.1016/j.sbi.2024.102868","DOIUrl":"https://doi.org/10.1016/j.sbi.2024.102868","url":null,"abstract":"<div><p>Double helical DNA winds around nucleosomes, forming a beads-on-a-string array that further contributes to the formation of high-order chromatin structures. The regulatory components of the chromatin, interacting intricately with DNA, often exploit the topological tension inherent in the DNA molecule. Recent findings shed light on, and simultaneously complicate, the multifaceted roles of DNA topology (also known as DNA supercoiling) in various aspects of chromatin regulation. Different studies may emphasize the dynamics of DNA topological tension across different scales, interacting with diverse chromatin factors such as nucleosomes, nucleic acid motors that propel DNA-tracking processes, and DNA topoisomerases. In this review, we consolidate recent studies and establish connections between distinct scientific discoveries, advancing our current understanding of chromatin regulation mediated by the supercoiling tension of the double helix. Additionally, we explore the implications of DNA topology and DNA topoisomerases in human diseases, along with their potential applications in therapeutic interventions.</p></div>","PeriodicalId":10887,"journal":{"name":"Current opinion in structural biology","volume":"87 ","pages":"Article 102868"},"PeriodicalIF":6.8,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141323753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0